Job ID = 6507728 SRX = SRX1353665 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-26T13:33:03 prefetch.2.10.7: 1) Downloading 'SRR2722819'... 2020-06-26T13:33:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:35:41 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:35:41 prefetch.2.10.7: 1) 'SRR2722819' was downloaded successfully Read 14247449 spots for SRR2722819/SRR2722819.sra Written 14247449 spots for SRR2722819/SRR2722819.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:13:16 14247449 reads; of these: 14247449 (100.00%) were paired; of these: 830551 (5.83%) aligned concordantly 0 times 11293607 (79.27%) aligned concordantly exactly 1 time 2123291 (14.90%) aligned concordantly >1 times ---- 830551 pairs aligned concordantly 0 times; of these: 270150 (32.53%) aligned discordantly 1 time ---- 560401 pairs aligned 0 times concordantly or discordantly; of these: 1120802 mates make up the pairs; of these: 763424 (68.11%) aligned 0 times 220621 (19.68%) aligned exactly 1 time 136757 (12.20%) aligned >1 times 97.32% overall alignment rate Time searching: 00:13:16 Overall time: 00:13:16 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 257967 / 13615921 = 0.0189 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 26 Jun 2020 22:58:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1353665/SRX1353665.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1353665/SRX1353665.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1353665/SRX1353665.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1353665/SRX1353665.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 26 Jun 2020 22:58:41: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:58:41: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:58:47: 1000000 INFO @ Fri, 26 Jun 2020 22:58:53: 2000000 INFO @ Fri, 26 Jun 2020 22:58:59: 3000000 INFO @ Fri, 26 Jun 2020 22:59:05: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 26 Jun 2020 22:59:11: 5000000 INFO @ Fri, 26 Jun 2020 22:59:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1353665/SRX1353665.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1353665/SRX1353665.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1353665/SRX1353665.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1353665/SRX1353665.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 26 Jun 2020 22:59:11: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:59:11: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:59:17: 6000000 INFO @ Fri, 26 Jun 2020 22:59:17: 1000000 INFO @ Fri, 26 Jun 2020 22:59:23: 2000000 INFO @ Fri, 26 Jun 2020 22:59:23: 7000000 INFO @ Fri, 26 Jun 2020 22:59:30: 3000000 INFO @ Fri, 26 Jun 2020 22:59:30: 8000000 INFO @ Fri, 26 Jun 2020 22:59:36: 4000000 INFO @ Fri, 26 Jun 2020 22:59:36: 9000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 26 Jun 2020 22:59:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1353665/SRX1353665.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1353665/SRX1353665.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1353665/SRX1353665.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1353665/SRX1353665.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 26 Jun 2020 22:59:41: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:59:41: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:59:42: 5000000 INFO @ Fri, 26 Jun 2020 22:59:43: 10000000 INFO @ Fri, 26 Jun 2020 22:59:48: 1000000 INFO @ Fri, 26 Jun 2020 22:59:48: 6000000 INFO @ Fri, 26 Jun 2020 22:59:50: 11000000 INFO @ Fri, 26 Jun 2020 22:59:55: 7000000 INFO @ Fri, 26 Jun 2020 22:59:55: 2000000 INFO @ Fri, 26 Jun 2020 22:59:57: 12000000 INFO @ Fri, 26 Jun 2020 23:00:01: 8000000 INFO @ Fri, 26 Jun 2020 23:00:02: 3000000 INFO @ Fri, 26 Jun 2020 23:00:03: 13000000 INFO @ Fri, 26 Jun 2020 23:00:07: 9000000 INFO @ Fri, 26 Jun 2020 23:00:08: 4000000 INFO @ Fri, 26 Jun 2020 23:00:10: 14000000 INFO @ Fri, 26 Jun 2020 23:00:13: 10000000 INFO @ Fri, 26 Jun 2020 23:00:15: 5000000 INFO @ Fri, 26 Jun 2020 23:00:17: 15000000 INFO @ Fri, 26 Jun 2020 23:00:20: 11000000 INFO @ Fri, 26 Jun 2020 23:00:22: 6000000 INFO @ Fri, 26 Jun 2020 23:00:24: 16000000 INFO @ Fri, 26 Jun 2020 23:00:26: 12000000 INFO @ Fri, 26 Jun 2020 23:00:29: 7000000 INFO @ Fri, 26 Jun 2020 23:00:31: 17000000 INFO @ Fri, 26 Jun 2020 23:00:32: 13000000 INFO @ Fri, 26 Jun 2020 23:00:36: 8000000 INFO @ Fri, 26 Jun 2020 23:00:38: 18000000 INFO @ Fri, 26 Jun 2020 23:00:38: 14000000 INFO @ Fri, 26 Jun 2020 23:00:43: 9000000 INFO @ Fri, 26 Jun 2020 23:00:44: 19000000 INFO @ Fri, 26 Jun 2020 23:00:44: 15000000 INFO @ Fri, 26 Jun 2020 23:00:49: 10000000 INFO @ Fri, 26 Jun 2020 23:00:51: 16000000 INFO @ Fri, 26 Jun 2020 23:00:51: 20000000 INFO @ Fri, 26 Jun 2020 23:00:56: 11000000 INFO @ Fri, 26 Jun 2020 23:00:57: 17000000 INFO @ Fri, 26 Jun 2020 23:00:58: 21000000 INFO @ Fri, 26 Jun 2020 23:01:03: 18000000 INFO @ Fri, 26 Jun 2020 23:01:03: 12000000 INFO @ Fri, 26 Jun 2020 23:01:05: 22000000 INFO @ Fri, 26 Jun 2020 23:01:09: 19000000 INFO @ Fri, 26 Jun 2020 23:01:10: 13000000 INFO @ Fri, 26 Jun 2020 23:01:12: 23000000 INFO @ Fri, 26 Jun 2020 23:01:15: 20000000 INFO @ Fri, 26 Jun 2020 23:01:16: 14000000 INFO @ Fri, 26 Jun 2020 23:01:18: 24000000 INFO @ Fri, 26 Jun 2020 23:01:21: 21000000 INFO @ Fri, 26 Jun 2020 23:01:23: 15000000 INFO @ Fri, 26 Jun 2020 23:01:25: 25000000 INFO @ Fri, 26 Jun 2020 23:01:28: 22000000 INFO @ Fri, 26 Jun 2020 23:01:30: 16000000 INFO @ Fri, 26 Jun 2020 23:01:32: 26000000 INFO @ Fri, 26 Jun 2020 23:01:34: 23000000 INFO @ Fri, 26 Jun 2020 23:01:37: 17000000 INFO @ Fri, 26 Jun 2020 23:01:38: 27000000 INFO @ Fri, 26 Jun 2020 23:01:40: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:01:40: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:01:40: #1 total tags in treatment: 13160174 INFO @ Fri, 26 Jun 2020 23:01:40: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:01:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:01:40: #1 tags after filtering in treatment: 12184225 INFO @ Fri, 26 Jun 2020 23:01:40: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 26 Jun 2020 23:01:40: #1 finished! INFO @ Fri, 26 Jun 2020 23:01:40: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:01:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:01:40: 24000000 INFO @ Fri, 26 Jun 2020 23:01:41: #2 number of paired peaks: 347 WARNING @ Fri, 26 Jun 2020 23:01:41: Fewer paired peaks (347) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 347 pairs to build model! INFO @ Fri, 26 Jun 2020 23:01:41: start model_add_line... INFO @ Fri, 26 Jun 2020 23:01:41: start X-correlation... INFO @ Fri, 26 Jun 2020 23:01:41: end of X-cor INFO @ Fri, 26 Jun 2020 23:01:41: #2 finished! INFO @ Fri, 26 Jun 2020 23:01:41: #2 predicted fragment length is 139 bps INFO @ Fri, 26 Jun 2020 23:01:41: #2 alternative fragment length(s) may be 4,139 bps INFO @ Fri, 26 Jun 2020 23:01:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1353665/SRX1353665.05_model.r INFO @ Fri, 26 Jun 2020 23:01:41: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:01:41: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:01:43: 18000000 INFO @ Fri, 26 Jun 2020 23:01:47: 25000000 INFO @ Fri, 26 Jun 2020 23:01:50: 19000000 INFO @ Fri, 26 Jun 2020 23:01:53: 26000000 INFO @ Fri, 26 Jun 2020 23:01:56: 20000000 INFO @ Fri, 26 Jun 2020 23:01:59: 27000000 INFO @ Fri, 26 Jun 2020 23:02:00: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:02:00: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:02:00: #1 total tags in treatment: 13160174 INFO @ Fri, 26 Jun 2020 23:02:00: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:02:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:02:01: #1 tags after filtering in treatment: 12184225 INFO @ Fri, 26 Jun 2020 23:02:01: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 26 Jun 2020 23:02:01: #1 finished! INFO @ Fri, 26 Jun 2020 23:02:01: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:02:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:02:01: #2 number of paired peaks: 347 WARNING @ Fri, 26 Jun 2020 23:02:01: Fewer paired peaks (347) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 347 pairs to build model! INFO @ Fri, 26 Jun 2020 23:02:01: start model_add_line... INFO @ Fri, 26 Jun 2020 23:02:02: start X-correlation... INFO @ Fri, 26 Jun 2020 23:02:02: end of X-cor INFO @ Fri, 26 Jun 2020 23:02:02: #2 finished! INFO @ Fri, 26 Jun 2020 23:02:02: #2 predicted fragment length is 139 bps INFO @ Fri, 26 Jun 2020 23:02:02: #2 alternative fragment length(s) may be 4,139 bps INFO @ Fri, 26 Jun 2020 23:02:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1353665/SRX1353665.10_model.r INFO @ Fri, 26 Jun 2020 23:02:02: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:02:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:02:02: 21000000 INFO @ Fri, 26 Jun 2020 23:02:08: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:02:08: 22000000 INFO @ Fri, 26 Jun 2020 23:02:14: 23000000 INFO @ Fri, 26 Jun 2020 23:02:19: 24000000 INFO @ Fri, 26 Jun 2020 23:02:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1353665/SRX1353665.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:02:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1353665/SRX1353665.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:02:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1353665/SRX1353665.05_summits.bed INFO @ Fri, 26 Jun 2020 23:02:21: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (525 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:02:25: 25000000 INFO @ Fri, 26 Jun 2020 23:02:29: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:02:31: 26000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:02:37: 27000000 INFO @ Fri, 26 Jun 2020 23:02:38: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:02:38: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:02:38: #1 total tags in treatment: 13160174 INFO @ Fri, 26 Jun 2020 23:02:38: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:02:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:02:38: #1 tags after filtering in treatment: 12184225 INFO @ Fri, 26 Jun 2020 23:02:38: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 26 Jun 2020 23:02:38: #1 finished! INFO @ Fri, 26 Jun 2020 23:02:38: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:02:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:02:39: #2 number of paired peaks: 347 WARNING @ Fri, 26 Jun 2020 23:02:39: Fewer paired peaks (347) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 347 pairs to build model! INFO @ Fri, 26 Jun 2020 23:02:39: start model_add_line... INFO @ Fri, 26 Jun 2020 23:02:39: start X-correlation... INFO @ Fri, 26 Jun 2020 23:02:39: end of X-cor INFO @ Fri, 26 Jun 2020 23:02:39: #2 finished! INFO @ Fri, 26 Jun 2020 23:02:39: #2 predicted fragment length is 139 bps INFO @ Fri, 26 Jun 2020 23:02:39: #2 alternative fragment length(s) may be 4,139 bps INFO @ Fri, 26 Jun 2020 23:02:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1353665/SRX1353665.20_model.r INFO @ Fri, 26 Jun 2020 23:02:39: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:02:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:02:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1353665/SRX1353665.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:02:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1353665/SRX1353665.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:02:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1353665/SRX1353665.10_summits.bed INFO @ Fri, 26 Jun 2020 23:02:42: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (290 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:03:06: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:03:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1353665/SRX1353665.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:03:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1353665/SRX1353665.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:03:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1353665/SRX1353665.20_summits.bed INFO @ Fri, 26 Jun 2020 23:03:18: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (188 records, 4 fields): 2 millis CompletedMACS2peakCalling